ri-autoregulation-extraction-v01.py
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# -*- coding: UTF-8 -*-
from optparse import OptionParser
import sys
import os
import json
import operator
import re
from general_functions import getTypeRegulation
from nltk.corpus import words
__author__ = 'CMendezC'
# Objective: obtain predicted ris from autoregulation sentences,
# such as ArgP protein represses its own synthesis
# Input format: transformed format.
# WARNING: Only one sentence per line
# Parameters:
# 1) --inputPath Input path
# 2) --inputFile Inpupt file
# 3) --outputPath Output path
# 5) --diccPath Dictionary path
# 7) --diccEffect File with normalized effects
# 6) --diccFile JSON file with entity dictionaries
# 9) --diccEPAth Dictionary path diccEffect
# 8) --format Output format: standoff, tabs
# Ouput:
# 1) File with predicted ris combined with existing files.
# Format standoff:
# T1 TF 0 0 ArgP
# T2 GENE 0 0 Argp -- > argP
# R1 Interaction.activator Target:T3 Agent:T1
# Sentence ArgP protein represses its own synthesis
# The FimZ transcription factor activates this promoter directly ,
# and it also positively regulates the transcription of its own gene
# FimZ is known to regulate the expression of its own gene positively
# FimZ also positively regulates its own transcription
# ArgP protein represses its own synthesis
# ArgP both represses its own transcription
# ArgP protein represses its own synthesis
# OxyR|OxyR|TF is|be|VBZ also|also|RB a|a|DT regulator|regulator|EFFECT
# of|of|IN its|its|PRP$ own|own|JJ expression|expression|NN
# Execution
# python3 ri-autoregulation-extraction-v01.py
# --inputPath /home/cmendezc/bitbucket_repositories/automatic-extraction-ris-gcs/rie-gce-system/automatic-extraction-STM-RIs-dataset/bries-bacterial-regulatory-interaction-extraction-system/autoregulation-sentences
# --inputFile dataSet_OnlyRI_sentences.auto.1017.txt
# --outputPath /home/cmendezc/bitbucket_repositories/automatic-extraction-ris-gcs/rie-gce-system/automatic-extraction-STM-RIs-dataset/bries-bacterial-regulatory-interaction-extraction-system/predicted-ris-gcs
# --diccPath /home/cmendezc/terminologicalResources
# --diccEffect normalized_Effects.json
# python3 ri-autoregulation-extraction-v01.py --inputPath /home/cmendezc/bitbucket_repositories/automatic-extraction-ris-gcs/rie-gce-system/automatic-extraction-STM-RIs-dataset/bries-bacterial-regulatory-interaction-extraction-system/autoregulation-sentences --inputFile dataSet_OnlyRI_sentences.auto.1017.txt --outputPath /home/cmendezc/bitbucket_repositories/automatic-extraction-ris-gcs/rie-gce-system/automatic-extraction-STM-RIs-dataset/bries-bacterial-regulatory-interaction-extraction-system/predicted-ris-gcs --diccPath /home/cmendezc/terminologicalResources --diccEffect normalized_Effects.json
###########################################################
# MAIN PROGRAM #
###########################################################
def getPosWord(wordPos, endPos, text, termList):
offsetStart = 0
wordNum = 0
listText = text.split()
for w in listText:
# if filenameBefore.find('000-2') > -1:
# print("Word {} in wordNum {} with wordPos {}".format(w, wordNum, wordPos))
if wordNum >= int(wordPos):
# for tok in word.split():
for t in termList:
# For entities starting word: if w == t or (w.startswith(t) and w not in regularWords):
if w == t:
return [w, offsetStart, offsetStart + len(w) - 1]
#else:
wordNum += 1
offsetStart += len(w) + 1
if wordNum > int(endPos):
return None
return None
def getIdEntity(aList, etype, idE):
entity = aList[0]
if etype == "EFFECT":
normalizedEffect = entity
#print("EFFECT: {}".format(entity))
if entity in hashNormalizedEffects:
normalizedEffect = hashNormalizedEffects[entity]
etype += "." + normalizedEffect
#print("etype: {}".format(etype))
entityPosStart = aList[1]
entityPosEnd = aList[2]
keyEntity = "{} {} {} {}".format(etype, entityPosStart, entityPosEnd, entity)
#print("keyEntity: {}".format(keyEntity))
if keyEntity not in hashEntities:
idE += 1
idEntity = "T{}".format(idE)
hashEntities[keyEntity] = idEntity
#print("New entity {}: {}".format(idEntity, keyEntity))
return idEntity, idE
else:
idEntity = hashEntities[keyEntity]
return idEntity, idE
def getIdInteraction(regulator, regulated, effect, idI, hashInt):
#print("hashInt: {}".format(hashInt))
keyInteraction = "{} {} {}".format(regulator, regulated, effect)
if keyInteraction not in hashInt:
idI += 1
idInteraction = "R{}".format(idI)
hashInt[keyInteraction] = idInteraction
#print("New interaction {}: {}".format(idInteraction, keyInteraction))
#return idInteraction, idI
else:
idInteraction = hashInt[keyInteraction]
return idInteraction, idI
def saveFiles(filename, hashE, hashI, s, effect):
if effect:
outputPath = os.path.join(options.outputPath, "complete-ris")
else:
outputPath = os.path.join(options.outputPath, "incomplete-ris")
with open(os.path.join(outputPath, filename[:filename.rfind(".")] + ".a1"), mode="w") as a1File:
#with open(os.path.join(outputPath, filename[:file.find(".")] + ".a1"), mode="a+") as a1File:
for k, v in sorted(hashE.items(), key=operator.itemgetter(1)):
aList = k.split()
a1File.write("{}\t{} {} {}\t{}\n".format(v, aList[0], aList[1], aList[2], aList[3]))
with open(os.path.join(outputPath, filename[:filename.rfind(".")] + ".a2"), mode="w") as a2File:
#with open(os.path.join(outputPath, filename[:file.find(".")] + ".a2"), mode="a+") as a2File:
for k, v in sorted(hashI.items(), key=operator.itemgetter(1)):
aList = k.split()
a2File.write("{}\tInteraction.{} Target:{} Agent:{}\n".format(v, aList[2], aList[1], aList[0]))
with open(os.path.join(outputPath, filename[:filename.rfind(".")] + ".txt"), mode="w") as txtFile:
txtFile.write(s)
def loadFileEntities(filename, outputPath, hashTemp):
#print("Start loadFileEntities")
idE = 1
try:
f = filename[:filename.rfind(".")] + ".a1"
# print("file entities: {}".format(f))
with open(os.path.join(outputPath, f), mode="r") as a1File:
for line in a1File:
line = line.strip('\n')
listLine1 = line.split('\t')
listLine2 = listLine1[1].split(' ')
etype = listLine2[0]
entityPosStart = listLine2[1]
entityPosEnd = listLine2[2]
entity = listLine1[2]
keyEntity = "{} {} {} {}".format(etype, entityPosStart, entityPosEnd, entity)
idEntity = listLine1[0]
if keyEntity not in hashTemp:
hashTemp[keyEntity] = idEntity
if int(idEntity[1:]) > idE:
idE = int(idEntity[1:])
except IOError:
print("IOError file: {}".format(os.path.join(outputPath, f)))
# idE = 1
return idE
def loadFileInteractions(filename, outputPath, hashTemp):
#print("Start loadFileInteractions")
idI = 1
try:
with open(os.path.join(outputPath, filename[:filename.rfind(".")] + ".a2"), mode="r") as a2File:
for line in a2File:
#print("Line a2: {}".format(line))
line = line.strip('\n')
listLine1 = line.split('\t')
listLine2 = listLine1[1].split(' ')
regulator = listLine2[2]
regulator = regulator[regulator.find(":") + 1:]
regulated = listLine2[1]
regulated = regulated[regulated.find(":") + 1:]
effect = listLine2[0]
effect = effect[effect.find(".") + 1:]
idInteraction = listLine1[0]
keyInteraction = "{} {} {}".format(regulator, regulated, effect)
if keyInteraction not in hashTemp:
hashTemp[keyInteraction] = idInteraction
if int(idInteraction[1:]) > idI:
idI = int(idInteraction[1:])
except IOError:
print("IOError file: {}".format(os.path.join(outputPath, filename[:filename.rfind(".")] + ".a2")))
# idI = 1
return idI
'''
def getTypeRegulation(effect_group, posini, sent, type_sent):
# To change regulation effect in such as:
# negative regulator --> repressor
# positively regulates --> activator
effect_ret = effect_group
#listEff = effect_ret.split('|')
if type_sent == "tra":
regexTypeEffectPosi = re.compile(r'(?<=positive\|(RB|JJ) )' + effect_ret)
regexTypeEffectNega = re.compile(r'(?<=negative\|(RB|JJ) )' + effect_ret)
if regexTypeEffectPosi.search(sent, posini - 12):
# Creo que no es necesario: effect_ret = "activator|{}|{}".format(listEff[1], listEff[2])
effect_ret = "activator"
print("Change regulation effect: {}".format(sent))
elif regexTypeEffectNega.search(sent, posini - 12):
# Creo que no es necesario: effect_ret = "repressor|{}|{}".format(listEff[1], listEff[2])
effect_ret = "repressor"
print("Change regulation effect: {}".format(sent))
return effect_ret
'''
def getRealPos(posStart, posEnd, lin):
return (posStart, posEnd)
def getRI(r, l):
regulator = r.group('regulator')
regulatorPos = getRealPos(r.start('regulator'), r.end('regulator'), l)
# We change TF name to GENE name
listRegulator = regulator.split('|')
regulatorWord = listRegulator[0]
regulated = regulatorWord[0].lower()+regulatorWord[1:]
regulated += "|{}|GENE".format(regulated)
regulatedPos = getRealPos(0, 0, l)
effect = r.group('effect')
# print("effect from group: {}".format(effect))
effectPos = getRealPos(r.start('effect'), r.end('effect'), l)
# To change regulation effect in:
# negative regulator --> repressor
# positively regulates --> activator
effect = getTypeRegulation(effect, r.start('effect'), l, "tra")
return [regulator + '|' + str(regulatorPos[0]) + '|' + str(regulatorPos[1]),
regulated + '|' + str(regulatedPos[0]) + '|' + str(regulatedPos[1]),
effect + '|' + str(effectPos[0]) + '|' + str(effectPos[1]), l]
if __name__ == "__main__":
# Parameter definition
parser = OptionParser()
parser.add_option("--inputPath", dest="inputPath",
help="Input path", metavar="PATH")
parser.add_option("--inputFile", dest="inputFile",
help="Input file", metavar="FILE")
parser.add_option("--outputPath", dest="outputPath",
help="Output path", metavar="PATH")
parser.add_option("--diccPath", dest="diccPath",
help="Path to read dictionaries", metavar="PATH")
parser.add_option("--diccEffect", dest="diccEffect",
help="File with normalized effects", metavar="FILE")
(options, args) = parser.parse_args()
#if len(args) > 0:
# parser.error("None parameter entered.")
# sys.exit(1)
# Printing parameter values
print('-------------------------------- PARAMETERS --------------------------------')
print("Input path: " + str(options.inputPath))
print("Input file: " + str(options.inputFile))
print("Output path: " + str(options.outputPath))
print("Path to read dictionaries: " + str(options.diccPath))
print("File with normalized effects: " + str(options.diccEffect))
# Loading normalized effects
print('Loading normalized effects (all)...')
hashNormalizedEffects = {}
with open(os.path.join(options.diccPath, options.diccEffect)) as diccFile:
hashNormalizedEffects = json.load(diccFile)
listEffects = []
for eff in hashNormalizedEffects.keys():
listEffects.append(eff)
effects = "|".join(listEffects)
#print("Effects: {}".format(effects))
files = {}
hashEntities = {}
hashInteractions = {}
hashInteractionsEffect = {}
idEntities = 1
idInteractions = 1
idInteractionsEffect = 1
# The FimZ transcription factor activates this promoter directly ,
# and it also positively regulates the transcription of its own gene
# FimZ is known to regulate the expression of its own gene positively
# FimZ also positively regulates its own transcription
# ArgP protein represses its own synthesis
# ArgP both represses its own transcription
# ArgP protein represses its own synthesis
# OxyR|OxyR|TF is|be|VBZ also|also|RB a|a|DT regulator|regulator|EFFECT
# of|of|IN its|its|PRP$ own|own|JJ expression|expression|NN
regexAutoRI = re.compile(
# r'(?P<regulator>[^|\s]+\|[^|]+\|TF).+(?P<effect>(' + effects + '))\|[^|]+\|EFFECT\s([^\s]\s){,4}its\|its\|PRP\$ own\|own\|JJ (gene|transcription|synthesis|expression)')
r'(?P<regulator>[^|\s]+\|[^|]+\|TF).+\s(?P<effect>(' + effects + '))\|[^|]+\|EFFECT\s([^\s]+\s){,5}its\|its\|PRP\$ own\|own\|JJ (gene|transcription|synthesis|expression)')
#r'(?P<regulator>[^|\s]+\|[^|]+\|TF)\s([^|\s]+\|[^|]+\|[^(TF)\s]+\s)+(?P<effect>(' + effects + '))\|[^|]+\|EFFECT\s([^\s]+\s){,5}its\|its\|PRP\$ own\|own\|JJ (gene|transcription|synthesis|expression)')
#r'(?P<regulator>[^|\s]+\|[^|]+\|TF)\s([^|\s]+\|[^|]+\|[^T][^F]\s)+(?P<effect>(' + effects + '))\|[^|]+\|EFFECT')
filename = options.inputFile
hashEntities = {}
hashInteractions = {}
hashInteractionsEffect = {}
idEntities = 1
idInteractions = 1
idInteractionsEffect = 1
outputPath = os.path.join(options.outputPath, "complete-ris")
idEntities = loadFileEntities(filename, outputPath, hashEntities)
idInteractionsEffect = loadFileInteractions(filename, outputPath, hashInteractionsEffect)
outputPath = os.path.join(options.outputPath, "incomplete-ris")
idInteractions = loadFileInteractions(filename, outputPath, hashInteractions)
listRIs = []
# print("Read autoregulation file")
with open(os.path.join(options.inputPath, options.inputFile)) as iFile:
for line in iFile:
line = line.rstrip('\n')
print("Buscando autoregulation")
result = regexAutoRI.search(line)
#print("result: {}".format(result))
if result:
lineTemp = result.string[result.end('regulator'):result.end(0)]
# print("lineTemp: {}".format(lineTemp))
result2 = regexAutoRI.search(lineTemp)
if result2:
print("Regulator {} regulated {} effect {}".format(result2.group('regulator'), result2.group('regulator'), result2.group('effect')))
listRIs.append(getRI(result2, line))
print("listRIs: {}".format(listRIs))
elif result:
print("Regulator {} regulated {} effect {}".format(result.group('regulator'), result.group('regulator'), result.group('effect')))
listRIs.append(getRI(result, line))
print("listRIs: {}".format(listRIs))
for ri in listRIs:
#print("ri: {}".format(ri))
if len(ri) != 4:
print("WARNING! corrupted list")
exit()
regulator = ri[0]
regulated = ri[1]
effect = ri[2]
line = ri[3]
listElem = regulator.split('|')
regulatorWord = listElem[0]
regulatorType = listElem[2]
regulatorStart = listElem[3]
regulatorEnd = listElem[4]
listElem = regulated.split('|')
regulatedWord = listElem[0]
regulatedType = listElem[2]
regulatedStart = listElem[3]
regulatedEnd = listElem[4]
listElem = effect.split('|')
effectWord = listElem[0]
effectType = "EFFECT"
effectStart = listElem[1]
effectEnd = listElem[2]
idRegulator, idEntities = getIdEntity([regulatorWord, regulatorStart, regulatorEnd], "TF", idEntities)
idRegulated, idEntities = getIdEntity([regulatedWord, regulatedStart, regulatedEnd], "GENE", idEntities)
idInteraction, idInteractions = getIdInteraction(idRegulator, idRegulated, "regulator",
idInteractions, hashInteractions)
idEffect, idEntities = getIdEntity([effectWord, effectStart, effectEnd], "EFFECT", idEntities)
idInteraction, idInteractionsEffect = getIdInteraction(idRegulator, idRegulated, idEffect,
idInteractionsEffect,
hashInteractionsEffect)
saveFiles(filename, hashEntities, hashInteractions, line, effect=False)
saveFiles(filename, hashEntities, hashInteractionsEffect, line, effect=True)